Abstract: This disclosure describes techniques to improve the accuracy of random access of data stored in polynucleotide sequence data storage systems. Primers used in polynucleotide sequence replication and amplification can be scored against a number of criteria that indicate the fitness of sequences of nucleotides to function as primers. Primers having scores that indicate a particular fitness to function as primers can be added to a specific group of primers. The primers from the group of primers can be used in amplification and replication of polynucleotide sequences that encode digital data. Additionally, an amount of overlap between primer targets and payloads encoding digital data can be determined. Minimizing the amount of overlap between primer targets and payloads can improve the efficiency of polynucleotide replication and amplification. The bits of the digital data can be randomized to minimize the amount of overlap between payloads encoding the digital data and primer targets.

Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.

Abstract: Systems and methods for collecting and processing physical space data for use while performing an image-guided surgical (IGS) procedure are provided. The system and method includes obtaining a computer model of a non-rigid structure of interest in a patient and performing a rigid alignment of the computer model and surface data in a patient space associated with at least a portion of the non-rigid structure. The system and method also include computing a deformation of the computer model that provides a non-rigid alignment of the computer model and surface data, the deformation computed using a set of boundary conditions defined for each node of the computer model based on the rigid alignment and a kernel function. Additionally, the system and method can include displaying data for facilitating the IGS procedure based on the deformation.

Abstract: Disclosed are methods of determining the likelihood of a subject having or developing a gastric cancer. The methods comprise measuring the expression level of at least one miRNA having at least 90% sequence identity with an miRNA as described herein in a non-cellular biofluid sample obtained from the subject, wherein differential expression of miRNA expression in the sample obtained from the subject, as compared to a control, may be indicative of the subject having gastric cancer and wherein the miRNA may be either an miRNA listed as “up-regulated” or an miRNA listed as “down-regulated”. Also disclosed is a method of determining the likelihood of a subject having or developing a stage of a gastric cancer.

Abstract: The present invention provides a method to rapidly screen tumor cells for invasive and metastatic characteristics, heterogeneity and their response to therapeutic agents, and provides a multi-well microinjection system for the automated imaging and microinjection of zebrafish embryos.

Abstract: The present invention provides methods and systems for identifying and classifying epitopes and use of that information to analyze proteins and peptides within proteins, especially potential epitopes, and to use the information to design synthetic peptides and proteins, analyze biopharmaceutical proteins, and diagnose autoimmune conditions. Peptides which are bound in MHC grooves comprise two sets of amino acids: those that face inwards into the groove and determine the binding affinity to the MHC molecule (the groove exposed motifs or GEM) and those which do not interact with the groove but rather are on the obverse side exposed outwardly to the T-cells (the T-cell exposed Motifs or TCEM). The present invention utilizes information related to the identity and physiochemical characteristics of the GEM and TCEM.

Abstract: The disclosed apparatus, systems and methods relate to estimating the rate of biodegradation of contaminants in the ground by measuring thermal gradients in the vadose zone where heat is produced by biodegradation reactions, and averaging over a full seasonal period, such as one year or one seasonal cycle, in which the groundwater temperatures and surface temperatures vary in a cyclical manner. Exemplary embodiments correct for the delay required by the heat being produced in the ground to reach the locations where the temperature gradients are measured, and also cancel out the signal noise caused by the changing surface and groundwater temperatures. In further embodiments, a mathematical model is provided to test the validity of the invention on two example sites.

Abstract: A classification of a level of cancer in an organism is determined by analyzing a biological sample of the organism. The biological sample comprises clinically-relevant DNA and other DNA. At least some of the DNA is cell-free in the biological sample. An amount of a first set of DNA fragments from the biological sample corresponding to each of a plurality of sizes is measured. A first value of a first parameter is calculated based on the amounts of DNA fragments at the plurality of sizes. The first value is compared to a reference value. A classification of a level of cancer in the organism is determined based on the comparison.

Abstract: The invention relates to determination of the profile of unbound free fatty acids (FFAu) in biological samples, such as human and animal blood specimens and plant and animal oils, by measuring the fluorescence response of sets of different fluorescently labeled fatty acid binding proteins (probes) that undergo a change in fluorescence ratio at 2 wavelengths upon binding an FFAu. Use of these profiles in human and animal disease, in basic research, in drug development and in industrial uses is disclosed.

Abstract: The present disclosure provides methods of preventing, delaying the progression of, treating or alleviating a symptom of, or otherwise ameliorating cancer in a subject by administering a recombinant polypeptide and an agent that reduces IL-10 to a subject in need thereof.

Abstract: Improved methods and systems for personal medical monitoring are disclosed. The monitoring yields status information pertaining to persons being monitored. Notifications, recommendations and/or actions can be initiated by examination or analysis of the status information. The status information can include health, position (location) and other information.

Abstract: A novel method to predict toxicity and dose-dependent effects of an agent based on transcriptomic data analysis, by determining a predictive toxicogenomics space (PTGS) score. The PTGS score helps to predict and model the toxicity of compounds typically consisting of chemicals, pharmaceuticals, cosmetics and agrochemicals. The invention further comprises methods of deriving the PTGS score, as well as computer programs to calculate PTGS scores.

Abstract: A biosensor system determines analyte concentration from an output signal generated from a light-identifiable species or a redox reaction of the analyte. The biosensor system compensates at least 50% of the total error in the output signal with a primary function and may compensate a portion of the residual error with at least one residual function. An SSP function may serve as the primary function, first residual function, or second residual function. Preferably, when the SSP function serves as the first residual function, the SSP function compensates at least 50% of the residual error remaining after primary compensation. Preferably, when the SSP function serves as the second residual function, the SSP function compensates at least 50% of the residual error remaining after primary and first residual compensation. The error compensation provided by the primary, first residual, and second residual functions may be adjusted with function weighing coefficients.

Abstract: Techniques for determining therapy scores for at least two of an anti-PD1 therapy, an anti-CTLA4 therapy, an IL-2 therapy, an IFN alpha therapy, an anti-cancer vaccine therapy, an anti-angiogenic therapy, and an anti-CD20 therapy. The techniques include determining, using sequencing data for the subject and information indicating distribution of biomarker values across one or more reference populations, a first set of normalized biomarker scores for a first set of biomarkers associated with a first therapy; and a second set of normalized biomarker scores for a second set of biomarkers associated with a second therapy; providing the first set of normalized biomarker scores as input to a statistical model to obtain a first therapy score for the first therapy; and providing the second set of normalized biomarker scores as input to the statistical model to obtain a second therapy score for the second therapy.

Abstract: An aspect includes aggregating a plurality of disparate datasets into a document store with semi-structured attributes that includes a plurality of documents specifying a plurality of different geo spatial locations and a plurality of different environmental parameters. Niche model layers are generated for the environmental parameters at the geospatial locations based on contents of the document store. The niche model layers include a model layer for each of the different environmental parameters. An additional niche model layer is created for a derived environmental parameter at the geospatial locations based at least in part on one of the previously generated niche model layers. A future geospatial location of a species is predicted based on environmental attributes of the species and contents of at least a subset of the niche model layers. The predicted future geospatial location of the species overlaid on a geographic map is output.

Abstract: An apparatus and a method for diagnosing a tumor are provided. A histogram generating section generates a histogram from a result of a measurement of fluorescence intensity of a suspension produced from a target sample. The histogram indicates a relation between the fluorescence intensity and the number of cells. A determination section detects an S phase fluorescence intensity range corresponding to S phase cells based on the fluorescence intensity corresponding to a peak of the number of cells in the histogram, detects an abnormal fluorescence intensity range corresponding to tumor cells, based on a change in the number of cells in the S phase fluorescence intensity range, and performs a diagnosis of a tumor in the target sample based on an index of the number of cells in a range defined by excluding the abnormal fluorescence intensity range from the S phase fluorescence intensity range.

Abstract: Techniques for generating therapy biomarker scores and visualizing same. The techniques include determining, using a patient's sequence data and distributions of biomarker values across one or more reference populations, a first set of normalized scores for a first set of biomarkers associated with a first therapy, and a second set of normalized scores for a second set of biomarkers associated with a second therapy, generating a graphical user interface (GUI) including a first portion associated with the first therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores; and a second portion associated with a second therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores; and displaying the generated GUI.

Abstract: Methods using DNA Methylation arrays are provided for identifying a cell or mixture of cells and for quantification of alterations in distribution of cells in blood or in tissues, and for diagnosing, prognosing and treating disease conditions, particularly cancer. The methods use fresh and archival samples.

Abstract: Exemplary systems, methods and computer accessible mediums which can determine quantitative information of a tissue(s) can be provided, which can include receiving optical information regarding the tissue(s), and determining the quantitative information of the tissue(s), in real time and during the receipt of the optical information, using an atlas. The tissue(s) can be part of a mouse, and the quantitative information can be an in-vivo count of cells or bacteria in the tissue(s). The quantitative information can be determined by co-registering the in-vivo count to the atlas. The optical information can be generated using a mirror gantry(s) so as to simultaneously image at least two opposing views of the tissue(s).

Abstract: Gene expression profiling in multiple myeloma patients identifies genes that distinguish between patients with subsequent early death or long survival after treatment. Poor survival is linked to over-expression of genes such as ASPM, OPN3 and CKS1B which are located in chromosome 1q. Given the frequent amplification of 1q in many cancers, it is possible that these genes can be used as powerful prognostic markers and therapeutic targets for multiple myeloma and other cancer.